rs13355682

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The variant allele was found at a frequency of 0.179 in 152,124 control chromosomes in the GnomAD database, including 2,643 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.18 ( 2643 hom., cov: 32)

Consequence

Unknown

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.887
Variant links:

Genome browser will be placed here

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.95).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.369 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt

Frequencies

GnomAD3 genomes
AF:
0.178
AC:
27128
AN:
152006
Hom.:
2634
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.209
Gnomad AMI
AF:
0.0724
Gnomad AMR
AF:
0.152
Gnomad ASJ
AF:
0.147
Gnomad EAS
AF:
0.384
Gnomad SAS
AF:
0.201
Gnomad FIN
AF:
0.190
Gnomad MID
AF:
0.117
Gnomad NFE
AF:
0.151
Gnomad OTH
AF:
0.174
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.179
AC:
27166
AN:
152124
Hom.:
2643
Cov.:
32
AF XY:
0.181
AC XY:
13460
AN XY:
74360
show subpopulations
Gnomad4 AFR
AF:
0.209
Gnomad4 AMR
AF:
0.152
Gnomad4 ASJ
AF:
0.147
Gnomad4 EAS
AF:
0.383
Gnomad4 SAS
AF:
0.200
Gnomad4 FIN
AF:
0.190
Gnomad4 NFE
AF:
0.151
Gnomad4 OTH
AF:
0.183
Alfa
AF:
0.159
Hom.:
400
Bravo
AF:
0.176
Asia WGS
AF:
0.305
AC:
1059
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.95
CADD
Benign
0.27
DANN
Benign
0.59

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs13355682; hg19: chr5-179791487; API